Galaxy Macromolecular Coarse-Grained Flexibility tutorial Version 1
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Run on GalaxyMacromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)
This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2023 Barcelona Supercomputing Center
- (c) 2015-2023 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Fetch structure | biobb_io_pdb_ext |
| 1 | ExtractAtoms | biobb_structure_utils_extract_atoms_ext |
| 2 | NmaRun | biobb_flexserv_nma_run_ext |
| 3 | DmdRun | biobb_flexserv_dmd_run_ext |
| 4 | BdRun | biobb_flexserv_bd_run_ext |
| 5 | CpptrajRms NMA | biobb_analysis_cpptraj_rms_ext |
| 6 | PczZip NMA | biobb_flexserv_pcz_zip_ext |
| 7 | CpptrajRms DMD | biobb_analysis_cpptraj_rms_ext |
| 8 | PczZip DMD | biobb_flexserv_pcz_zip_ext |
| 9 | CpptrajRms BD | biobb_analysis_cpptraj_rms_ext |
| 10 | PczZip BD | biobb_flexserv_pcz_zip_ext |
| 11 | PczUnzip NMA | biobb_flexserv_pcz_unzip_ext |
| 12 | PczBfactor NMA | biobb_flexserv_pcz_bfactor_ext |
| 13 | PczAnimate NMA | biobb_flexserv_pcz_animate_ext |
| 14 | PczInfo NMA | biobb_flexserv_pcz_info_ext |
| 15 | PczEvecs NMA | biobb_flexserv_pcz_evecs_ext |
| 16 | PczStiffness NMA | biobb_flexserv_pcz_stiffness_ext |
| 17 | PczCollectivity NMA | biobb_flexserv_pcz_collectivity_ext |
| 18 | PczUnzip DMD | biobb_flexserv_pcz_unzip_ext |
| 19 | PczUnzip BD | biobb_flexserv_pcz_unzip_ext |
| 20 | PczHinges DynDon | biobb_flexserv_pcz_hinges_ext |
| 21 | PczHinges Bfactor | biobb_flexserv_pcz_hinges_ext |
| 22 | PczHinges FCTE | biobb_flexserv_pcz_hinges_ext |
| 23 | CpptrajRms NMA 2 | biobb_analysis_cpptraj_rms_ext |
| 24 | CpptrajConvert NMA | biobb_analysis_cpptraj_convert_ext |
| 25 | CpptrajRms DMD 2 | biobb_analysis_cpptraj_rms_ext |
| 26 | CpptrajRms BD 2 | biobb_analysis_cpptraj_rms_ext |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
|
| _anonymous_output_13 | #main/_anonymous_output_13 | n/a |
|
| _anonymous_output_14 | #main/_anonymous_output_14 | n/a |
|
| _anonymous_output_15 | #main/_anonymous_output_15 | n/a |
|
| _anonymous_output_16 | #main/_anonymous_output_16 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
| bd_ensemble.log | #main/bd_ensemble.log | n/a |
|
| bd_ensemble.mdcrd | #main/bd_ensemble.mdcrd | n/a |
|
| bd_ensemble.pcz | #main/bd_ensemble.pcz | n/a |
|
| bd_ensemble_rmsd.dat | #main/bd_ensemble_rmsd.dat | n/a |
|
| bd_ensemble_rmsd.dcd | #main/bd_ensemble_rmsd.dcd | n/a |
|
| bd_ensemble_uncompressed.crd | #main/bd_ensemble_uncompressed.crd | n/a |
|
| bfactor_all.dat | #main/bfactor_all.dat | n/a |
|
| bfactor_all.pdb | #main/bfactor_all.pdb | n/a |
|
| dmd_ensemble.log | #main/dmd_ensemble.log | n/a |
|
| dmd_ensemble.mdcrd | #main/dmd_ensemble.mdcrd | n/a |
|
| hinges_bfactor_report.json | #main/hinges_bfactor_report.json | n/a |
|
| mypdb.pdb | #main/mypdb.pdb | n/a |
|
| nma_ensemble.log | #main/nma_ensemble.log | n/a |
|
| nma_ensemble.mdcrd | #main/nma_ensemble.mdcrd | n/a |
|
| pcz_collectivity.json | #main/pcz_collectivity.json | n/a |
|
| pcz_evecs.json | #main/pcz_evecs.json | n/a |
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| pcz_proj1.crd | #main/pcz_proj1.crd | n/a |
|
| pcz_proj1.dcd | #main/pcz_proj1.dcd | n/a |
|
| pcz_report.json | #main/pcz_report.json | n/a |
|
| pcz_stiffness.json | #main/pcz_stiffness.json | n/a |
|
| structure_ca.pdb | #main/structure_ca.pdb | n/a |
|
Version History
Version 1 (earliest) Created 11th Aug 2023 at 09:32 by Genís Bayarri
Initial commit
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Version-18b2c420
Creators and Submitter
Views: 3280 Downloads: 466 Runs: 0
Created: 11th Aug 2023 at 09:32
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
